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iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets2022 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, +7 more
102citations -
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins2020 PLoS ONE article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham
4citations -
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors2023 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access
Marina Gorostiola González, Remco L. van den Broek, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, +1 more
6citations -
The Role of IgM Anti‐acetylated Protein Antibodies and B Cells in the Origin of Antimodified Protein Autoimmunity in Rheumatoid Arthritis2026 Arthritis & Rheumatology article Medicine Rheumatoid Arthritis Research and Therapies Open access
Aegli Athanasiadou, Sanne Kroos, Renee van de Wetering, Rian Schopmeijer, Carin van der Keur, Michael Eikmans, +5 more
0citations -
Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut2025 Nature Communications article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Matthias A. Schmitz, Nicholas J Dimonaco, Thomas Clavel, Thomas C. A. Hitch
9citations -
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access cited by 2 patents
Amelia Villegas-Morcillo, Stavros Makrodimitris, Roeland C. H. J. van Ham, Angel Manuel Gomez, Marcel J. T. Reinders
137citations -
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort2024 Journal of Chemical Information and Modeling article Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics
Alexander-Maurice Illig, Niklas E. Siedhoff, Mehdi D. Davari, Ulrich Schwaneberg
3citations -
Should LC-MS/MS Be the Reference Measurement Procedure to Determine Protein Concentrations in Human Samples?2020 Clinical Chemistry article Medicine Clinical Laboratory Practices and Quality Control Open access
Andrew N. Hoofnagle, Christa M. Cobbaert, Vincent Delatour, Neil L. Kelleher, Mark S. Lowenthal, Christopher M. Shuford
27citations -
Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation2025 The Journal of Physical Chemistry B article Biochemistry, Genetics and Molecular Biology DNA and Nucleic Acid Chemistry Open access
Thor van Heesch, Sudhanshu Sharma, Bert van Erp, Alberto Pérez de Alba Ortíz, Remus Thei Dame, Jocelyne Vreede, +1 more
2citations -
PyTEA-O: a Python implementation of Two-Entropies Analysis for protein sequence variation analysis2026 Bioinformatics article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Rosan C.M. Kuin, Alexander Thomas Julian, J Chander, S Lee, Gerard J. P. van Westen
2citations -
Isotope Decluttering Reduces Spectral Complexity while Maintaining Protein Structure2026 Analytical Chemistry article Chemistry Mass Spectrometry Techniques and Applications Open access
Sneha Hakke, Willem E. M. Noteborn, Birol Cabukusta, Ye Gao, Kèvin Knoops, Carmen López‐Iglesias, +4 more
0citations -
Gene and protein sequence features augment HLA class I ligand predictions2024 Cell Reports article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Kaspar Bresser, Benoît P. Nicolet, Anita Jekő, Wei Wu, Fabricio Loayza‐Puch, Reuven Agami, +3 more
4citations -
Podocyte Integrin-β 3 and Activated Protein C Coordinately Restrict RhoA Signaling and Ameliorate Diabetic Nephropathy2020 Journal of the American Society of Nephrology article Medicine Renal Diseases and Glomerulopathies Open access
Thati Madhusudhan, Sanchita Purohit Ghosh, Wei Dong, Dheerendra Gupta, Ahmed Elwakiel, Stoyan Stoyanov, +17 more
27citations -
mRNA Expression Level of ALK in Neuroblastoma Is Associated with Histological Subtype, ALK Mutations and ALK Immunohistochemical Protein Expression2024 Journal of Molecular Pathology article Medicine Neuroblastoma Research and Treatments Open access
Rixt S. Bruinsma, Marta F. Fiocco, Wendy W.J. de Leng, Lennart A. Kester, Karin P.S. Langenberg, Godelieve A.M. Tytgat, +4 more
1citations -
A CRISPR /Cas9‐based multicopy integration system for protein production in Aspergillus niger2023 FEBS Journal article Biochemistry, Genetics and Molecular Biology Fungal and yeast genetics research Open access
Mark Arentshorst, Prajeesh Kooloth-Valappil, László Mózsik, Tonny J. G. Regensburg‐Tuïnk, Sjoerd J. Seekles, Gwen Tjallinks, +3 more
29citations -
Evolutionary Engineering of a Cp*Rh(III) Complex-Linked Artificial Metalloenzyme with a Chimeric β-Barrel Protein Scaffold2023 Journal of the American Chemical Society article Chemistry Cyclopropane Reaction Mechanisms Open access
Shunsuke Kato, Akira Onoda, Ulrich Schwaneberg, Takashi Hayashi
28citations -
Predicting high recombinant protein producer strains of Pichia pastoris MutS using the oxygen transfer rate as an indicator of metabolic burden2022 Scientific Reports article Biochemistry, Genetics and Molecular Biology Fungal and yeast genetics research Open access
David Wollborn, Lara Pauline Munkler, Rebekka Horstmann, Andrea Germer, Lars M. Blank, Jochen Büchs
17citations -
A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation2020 Chemical Science article Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Liubov Yakovlieva, Johan Kemmink, Ioli Kotsogianni, Franziska Koller, Jürgen Lassak, Nathaniel I. Martin, +1 more
9citations -
PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction2024 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada
41citations